CCDC59

protein-coding

coiled-coil domain containing 59

Gene summary

Enables RNA binding activity. Predicted to be involved in DNA-templated transcription. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014167.5

Inheritance

—

ClinVar variants

U:42B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.13

Max pathogenic AF

—

Genomic locus

chr12:82,223,681-82,358,805

External References & Databases

Ensembl (ENSG00000133773)

Transcript & Mutation Effects

hg38 • Region Span ~135.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC59 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 39

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014167.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			40 clinvar	1 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	42	1	0	43

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014167.5	RefSeq	NP_054886.2	4	MANE Select
ENST00000256151.8	Ensembl	ENSP00000256151.7	4	MANE Select
ENST00000552377.5	Ensembl	ENSP00000450183.1	4	Standard
ENST00000930495.1	Ensembl	ENSP00000600554.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Surfactant metabolism
Metabolism of proteins

Biological Process

cellular protein metabolic process

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000256151
Coding exons: 4
Length: 135125
Individuals with no LoFs: 125349
Homozygous LoFs: 0
Heterozygous LoFs: 399
Defined: 125748
p: 0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.37	167	124	1.34	0.00000613	1583
Missense (PolyPhen)		47	38.116	1.2331		547
Synonymous	-0.968	56	47.5	1.18	0.00000250	416
Loss of Function	-0.426	15	13.3	1.13	6.97e-7	159

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00055	rare
Latino/Admixed American	0.00043	0.00040	rare
Ashkenazi Jewish	0.0015	0.0014	notable
East Asian	0.00060	0.00060	rare
Finnish	0.0036	0.0034	notable
European (Non-Finnish)	0.0025	0.0022	notable
South Asian	0.00048	0.00042	rare
Other	0.0020	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the transcription complexes of the pulmonary surfactant-associated protein-B (SFTPB) and -C (SFTPC). Enhances homeobox protein Nkx-2.1-activated SFTPB and SFTPC promoter activities. {ECO:0000269|PubMed:12882447, ECO:0000269|PubMed:16630564}.;

Recessive Scores

pRec: 0.0959

Intolerance Scores

LoFtool: 0.384
RVIS EVS: 1.06
RVIS percentile EVS: 91.47

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.633

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium